Microflora in teeth associated with apical periodontitis: a methodological observational study comparing two protocols and three microscopy techniques

How to study biofilms: technological advancements in clinical biofilm research

Biofilm formation is an important survival strategy commonly used by bacteria and fungi, which are embedded in a protective extracellular matrix of organic polymers. They are ubiquitous in nature, including humans and other animals, and they can be surface- and non-surface-associated, making them capable of growing in and on many different parts of the body. Biofilms are also complex, forming polymicrobial communities that are difficult to eradicate due to their unique growth dynamics, and clinical infections associated with biofilms are a huge burden in the healthcare setting, as they are often difficult to diagnose and to treat. Our understanding of biofilm formation and development is a fast-paced and important research focus. This review aims to describe the advancements in clinical biofilm research, including both in vitro and in vivo biofilm models, imaging techniques and techniques to analyse the biological functions of the biofilm.

Ageing-related effects of dye penetration in the apical 5 mm mesiobuccal and mesial roots of molars

This study examined how the tubular permeability in the apical 5 mm of mesial roots was affected by age, direction, distance from root apex, canal shape and canal number. Twenty mesiobuccal/mesial roots of maxillary/mandibular molars from three age groups (<30, 30-60, >60 years) were prepared. Maximal dye penetration in buccal, lingual, mesial and distal directions was measured at 1-mm segment depth and analysed statistically. The <30 years group, when comparing to the >60 years group, had significantly deeper dye penetration in buccal and lingual directions. The permeability in proximal directions was not affected by either age or canal number. In the >60 years group, neither direction, segment depth nor canal number significantly impacted the permeability. However, these parameters significantly impacted samples younger than 60 years. Effective removal of infected root canal dentine would depend on age and its related preferred direction, distance from root apex and canal number.

Bacteria in the cavity-restoration interface after varying periods of clinical service - SEM description of distribution and 16S rRNA gene sequence identification of isolates

OBJECTIVES

To use extracted human teeth with amalgam (n = 26) or GIC (n = 3) restorations in service up to 20 years to evaluate microbiota at the cavity/restoration interface by SEM or culture.

MATERIALS AND METHODS

Extracted teeth with intracoronal restorations (n = 20) of known history (2-20 years) were fixed, split, and prepared for SEM to ascertain the pattern and structure of bacterial aggregates on cavity and restoration surfaces. Another 9 teeth were anaerobically decontaminated, split and sampled (cavity/restorations), and cultured (anaerobically, aerobically); recovered isolates were identified by 16S rRNA gene sequencing.

RESULTS

SEM showed rods, cocci, and filaments in 11/20 teeth (55%) on cavity and corresponding restoration surfaces; 4/20 (20%) on neither surface; 1/20 (5%) on just cavity; and 4/20 (20%) on just restoration. Microbial growth extended from marginal openings into the deeper interfacial microspace to varying extents but was not always evident. Restoration size or age did not predict bacterial presence. Bacteria-free surfaces (cavity/amalgam) showed possible calcification. Cultivation yielded 160 isolates, mainly Gram-positive (86%) and facultative (81%); and morphotypes of rods (43%), cocci (36%), and cocco-bacilli (18%) belonging to Actinobacteria (45%) and Firmicutes (50%). The most frequent genera were Staphylococcus, Streptococcus, Actinomyces, and Lactobacillus. Biofilms on cavity and restoration appeared independent of each other.

CONCLUSIONS

Cavity and amalgam surfaces were independently colonised and some not. The penetration of microbiota into marginal gaps varied; resembled root caries and was dominated by Gram-positive species.

CLINICAL RELEVANCE

Marginal gaps around restorations are unavoidable but are not always colonised by bacteria after long-term clinical service. Calcification of biofilms in the restorative interface may prevent further colonisation. The viable microbiota in the restorative interface resembled root caries and may be subject to ecological fluxes of activity and arrest and therefore preventative management.

An In Vitro Model to Study the Colonization and Tubular Invasion of Enterococcus faecalis

INTRODUCTION

The purpose of this study was to examine the colonization and tubular invasion of Enterococcus faecalis in minimally altered canal walls. We hypothesized that age, axial directions (buccolingual or mesiodistal), regions (apical, midroot, or cervical), and disinfection treatment (sodium hypochlorite or autoclave) would impact bacterial colonization and invasion patterns.

METHODS

Single roots of extracted teeth from 2 age groups (≤30 years old and ≥60 years old) were challenged with bacteria for 2 weeks. Colonization on the canal walls in 3 regions was evaluated with scanning electron microscopy. The prevalence of tubular invasion in the axial directions in 3 regions was examined with confocal laser scanning microscopy. The data were analyzed using the GLIMMIX procedure in SAS software (SAS Institute Inc, Cary, NC) with a Tukey adjustment for comparisons.

RESULTS

Bacteria successfully colonized and invaded tubules in 2 weeks. The apical region in the ≥60-year age group was the least infected. A significantly higher invasion prevalence in a buccolingual (B/L) than a mesiodistal (M/D) direction was detected in both age groups and in all 3 regions. The ≤30-year age group had a significantly higher prevalence of tubular invasion than the ≥60-year age group in the B/L and M/D direction, respectively. Sodium hypochlorite treatment significantly impacted bacterial colonization and invasion in more calcified areas.

CONCLUSIONS

Our data support a more conservative enlargement of the apical region of older teeth. An emphasis in a B/L direction rather than an M/D direction is recommended for debridement.

Microscopy Methods for Biofilm Imaging: Focus on SEM and VP-SEM Pros and Cons

Simple Summary

Bacterial biofilms cause infections that are often resistant to antibiotic treatments. Research about the formation and elimination of biofilms cannot be undertaken without detailed imaging techniques. In this review, traditional and cutting-edge microscopy methods to study biofilm structure, ultrastructure, and 3-D architecture, with particular emphasis on conventional scanning electron microscopy and variable pressure scanning electron microscopy, are addressed, with the respective advantages and disadvantages. When ultrastructural characterization of biofilm matrix and its embedded bacterial cells is needed, as in studies on the effects of drug treatments on biofilm, scanning electron microscopy with customized protocols such as the osmium tetroxide (OsO₄), ruthenium red (RR), tannic acid (TA), and ionic liquid (IL) must be preferred over other methods for the following: unparalleled image quality, magnification and resolution, minimal sample loss, and actual sample structure preservation. The first step to make a morphological assessment of the effect of the various pharmacological treatments on clinical biofilms is the production of images that faithfully reflect the structure of the sample. The extraction of quantitative parameters from images, possible using specific software, will allow for the scanning electron microscopy morphological evaluation to no longer be considered as an accessory technique, but a quantitative method to all effects.

Abstract

Several imaging methodologies have been used in biofilm studies, contributing to deepening the knowledge on their structure. This review illustrates the most widely used microscopy techniques in biofilm investigations, focusing on traditional and innovative scanning electron microscopy techniques such as scanning electron microscopy (SEM), variable pressure SEM (VP-SEM), environmental SEM (ESEM), and the more recent ambiental SEM (ASEM), ending with the cutting edge Cryo-SEM and focused ion beam SEM (FIB SEM), highlighting the pros and cons of several methods with particular emphasis on conventional SEM and VP-SEM. As each technique has its own advantages and disadvantages, the choice of the most appropriate method must be done carefully, based on the specific aim of the study. The evaluation of the drug effects on biofilm requires imaging methods that show the most detailed ultrastructural features of the biofilm. In this kind of research, the use of scanning electron microscopy with customized protocols such as osmium tetroxide (OsO₄), ruthenium red (RR), tannic acid (TA) staining, and ionic liquid (IL) treatment is unrivalled for its image quality, magnification, resolution, minimal sample loss, and actual sample structure preservation. The combined use of innovative SEM protocols and 3-D image analysis software will allow for quantitative data from SEM images to be extracted; in this way, data from images of samples that have undergone different antibiofilm treatments can be compared.

Microbial ecology and predicted metabolic pathways in various oral environments from patients with acute endodontic infections

AIM

To assess in a cross-sectional clinical study the effect of antibiotics on the diversity, structure and metabolic pathways of bacterial communities in various oral environments in patients with acute primary infections.

METHODOLOGY

Samples of saliva (SA), supragingival biofilm (SB) and from the pulp cavity (PC) were collected from teeth with acute primary infections and then grouped according to previous use of antibiotics (NoAtb = no antibiotics [n = 6]; Atb = antibiotics [n = 6]). DNA sequencing was conducted using MiSeq (Illumina, San Diego, CA, USA). The V1-V3 hyper-variable region of the 16S rRNA gene was amplified. A custom Mothur pipeline was used for 16S rRNA processing. Subsequent analyses of the sequence dataset were performed in R (using vegan, phyloseq and ggplot2 packages) or QIIME.

RESULTS

Twelve patients aged from 22 to 56 years were recruited. Participants in the Atb group had taken the beta-lactamics amoxicillin (5/6) or cephalexin (1/6) for 2-3 days. A total of 332 bacterial taxa (OTUs) were identified, belonging to 120 genera, 60 families and nine phyla. Firmicutes (41%) and Bacteroidetes (38%) were the most abundant phyla in all samples. Taxa clustered significantly by oral site (PCoA analysis; P < 0.05, ANOSIM). Use of antibiotics had little effect on this clustering. However, SA, SB and PC had different degrees of richness, diversity and evenness. The greatest diversity was observed in SB samples and the least diversity was observed in PC samples. Metabolic prediction identified 163 pathways and previous use of antibiotics had a major effect on the estimated functional clustering in SA and PC samples.

CONCLUSION

The ecological niche had a strong influence on the bacterial content of samples from various oral sites. Previous exposure to antibiotics may exert an effect on the phylogenetic composition of SA. Metabolic pathways appear to be modulated by antimicrobial agents in SA and PC samples. The dynamics of host/microbial interactions in the apical region and the functional ecology of the infected pulp cavity should be revisited.

Endodontic management of a three-rooted maxillary premolar: A case report

Maxillary premolars exhibit anatomical variations in the numbers of roots and canals, which pose a challenge during root canal therapy. In the present case report, we describe the endodontic management of a three-rooted maxillary premolar. A 47-year-old Yamani man was referred to the College of Dentistry, Taibah University for endodontic treatment of his right maxillary first premolar (#14). Periapical diagnostic radiography did not provide adequate information about the morphology of the root canal system and number of roots. Subsequently, a 3D cone-beam computed tomographic (CBCT) image was obtained, which revealed three roots in the aforementioned premolar. Root canal treatment was performed under magnification using a dental operating microscope, R25 RECIPROC blue NiTi single file system, and the Calamus dual 3-D obturation system. Clinicians should be able to predict the anatomical variations in maxillary premolars and have adequate knowledge and skills for managing such situations.

Efficacy of different carriers for the triple antibiotic powder during regenerative endodontic procedures

Chemical debridement during Regenerative Endodontic procedures is important. Previous research studies have evaluated various antibiotics and their concentrations but none have addressed the concern of delivering these materials. Hence, the purpose of this study was to determine what carrier could be used effectively in a clinical setting. Sixty caries-free maxillary incisors were used and inoculated with Enterococcus faecalis and divided into positive and irrigation controls and experimental groups that had triple antibiotic powder (1:1:1 ciprofloxacin:metronidazole:minocycline) delivered using various carriers: saline, cotton, sponge and methylcellulose. Current AAE regenerative protocols were followed. S2 sampling was performed and tested for bacterial presence via culturing and SEM. The results demonstrated that saline was the most effective carrier for the triple antibiotic powder while cotton and sponge were most ineffective. Saline and methylcellulose both reduced bacterial counts to a significant level. Overall, this study demonstrated that saline as a carrier was most effective and should be routinely used.

Prevalence and nature of fungi in root canal infections: a systematic review and meta-analysis

The role of bacteria in causing apical periodontitis has been widely established, whilst the role of other microorganisms is studied less thoroughly. This systematic review and meta-analysis reviewed the literature for the prevalence and diversity of fungi in root canal infections. An extensive literature search was carried out in the Cochrane databases, EMBASE, MEDLINE, LILACS, SciELO and Web of Science. Additional studies were identified from six endodontic journals, four main endodontic textbooks and references of relevant papers. Selected clinical studies included sampling of necrotic pulps in permanent teeth and microbial analysis of these samples. Studies were critically appraised using the Joanna Briggs Institute Prevalence Critical Appraisal Checklist. Meta-analysis was performed using MetaXL. The screening of 1041 titles and abstracts and full-text reading yielded 54 studies. The overall prevalence of fungi in root canal infections was 7.5% (CI 95%: 3.6-11.8%) in the inverse variance fixed effect heterogeneity model. Candida albicans was the most frequently isolated species. Significant heterogeneity was observed (P < 0.001, I²  = 85.04%). Subgroup analyses based on geographical location, period of publication, type of infection, state of general health, communication with the oral cavity, type of sample and identification method revealed no factor influencing the prevalence. Better standardized techniques and a comprehensive analysis will reveal a more detailed and accurate representation of the prevalence and nature of fungi in root canal infections.

Critical review on biofilm methods

Biofilms are widespread in nature and constitute an important strategy implemented by microorganisms to survive in sometimes harsh environmental conditions. They can be beneficial or have a negative impact particularly when formed in industrial settings or on medical devices. As such, research into the formation and elimination of biofilms is important for many disciplines. Several new methodologies have been recently developed for, or adapted to, biofilm studies that have contributed to deeper knowledge on biofilm physiology, structure and composition. In this review, traditional and cutting-edge methods to study biofilm biomass, viability, structure, composition and physiology are addressed. Moreover, as there is a lack of consensus among the diversity of techniques used to grow and study biofilms. This review intends to remedy this, by giving a critical perspective, highlighting the advantages and limitations of several methods. Accordingly, this review aims at helping scientists in finding the most appropriate and up-to-date methods to study their biofilms.

[Efficacy of sodium hydroxide at 2.5 %, chlorhexidine gluconate at 0.5 % and calcium hydroxide against Candida albicans]

INTRODUCTION

Endodontic flora is dominated in the apical part of the channels by strict anaerobic and some facultative anaerobic bacteria but also by Candida yeasts, especially Candida albicans species that are involved in the maintenance and persistence of endodontic infections. Their elimination of the canal system in practice by chemo-mechanical methods of disinfection is not always guaranteed. Thus, this in vitro study was performed to determine the sensitivity of C. albicans with sodium hypochlorite (NaOCl) dosed at 2.5 %, the chlorhexidine digluconate 0.5 % and calcium hydroxide used in inter-session medication.

METHODS

The diffusion method was used initially to test the sensitivity of C. albicans strains with the above products. Then a dilution technique has allowed us to determine the minimum inhibitory concentration of these active products on C. albicans.

RESULTS

Strains from infected pulp teeth of patients showed a sensitivity of C. albicans to sodium hypochlorite to a minimum inhibitory concentration less than 70μg/mL and 30μg/mL for chlorhexidine.

CONCLUSION

This study demonstrated a sensitivity of C. albicans to sodium hypochlorite and chlorhexidine.

Supplementary sampling of obturation materials enhances microbial analysis of endodontic treatment failures: a proof of principle study

OBJECTIVES

Root canal treatment failures often correlate with persistent biomaterial-associated endodontic infections. The aim of the present study was to assess the impact of endodontic obturation material sampling from root canals with posttreatment apical periodontitis on improving standard study protocols.

MATERIALS AND METHODS

Samples from previously filled root canals and their corresponding endodontic filling materials were obtained from five root-filled teeth with posttreatment periradicular lesions. After cultivation, the isolated microorganisms were quantified and biochemically identified. Moreover, clone libraries were constructed after the amplification of bacterial 16S ribosomal DNA (rDNA) from the same samples. DNA from selected clones was sequenced to identify microbial species. Transmission electron microscopy (TEM) aided visualization of the detected bacteria.

RESULTS

Overall, 22 taxa of the phyla Firmicutes, Actinobacteria, and Bacteroidetes were detected in both obturation and root canal samples by culture-dependent and culture-independent methods. Root canal fillings sheltered 17 species (3.30-7.50 × 10(3) CFU/ml). Of these, nine were detected solely in the retrieved obturation materials. The reinfected root canals harbored 13 taxa (3.48-7.36 × 10(3) CFU/ml). Obligate and facultative anaerobic bacteria prevailed. The number of different species ranged from 1 to 5 within a single sample. Fungi were not detected.

CONCLUSIONS

Bacteria can colonize both root canals and endodontic fillings in vivo.

CLINICAL RELEVANCE

Integrating the sampling of obturation materials with standard root canal sample collection offers a clearer insight into the actual microbial flora of reinfected root canals and improves the study protocols of secondary/persistent endodontic infections.

The presence and distribution of bacteria in dentinal tubules of root filled teeth

AIM

To investigate the distribution of bacteria within the dentine tubular network in a two-chamber model in order to determine a possible route of penetration.

METHODOLOGY

Root canals of teeth in the experimental group (n = 16) were instrumented and root filled using AH26 and gutta-percha. Canals in the teeth serving as positive (n = 1) and negative (n = 1) controls were instrumented, but not root filled. A two-chamber model was fabricated for each root - upper chambers were inoculated weekly with Streptococcus gordonii in brain-heart infusion broth over 90 days. Turbidity of the lower chamber was checked daily. Samples that showed turbidity during the experimental period and samples that showed no signs of turbidity at 90 days were fractured and prepared for SEM examination. SEM examination for the presence of bacteria within the dentinal tubules was performed in the cervical, middle and apical root thirds. In each root third, the depth of bacterial penetration was recorded as inner, middle or outer dentine.

RESULTS

Bacteria were most commonly detected in the cervical third (14 of 30 areas). Irrespective of the root third examined, bacteria were most commonly detected in the inner dentine (i.e. adjacent to the root canal). Only two samples demonstrated bacterial penetration in the outer dentine.

CONCLUSION

The dentine tubular network provides a potential pathway for bacteria to penetrate tooth roots in a two-chamber model.

An investigation of a potential confounder in ex vivo microbiological studies--the bulk flow of fluid through apical foramina during tooth extraction

AIMS

To investigate the factors affecting bulk flow of dye and bacterial suspensions into and out of apical foramina during simulated tooth extraction, using an ex vivo model.

METHODOLOGY

Sixty extracted, single-rooted, human teeth were accessed, root canals located and in 50 the pulps dissolved; 10 teeth with attached periapical lesions were preserved. The size of apical foramina was determined digitally. The teeth were mounted in vials with polyvinylsiloxane impression material. Part 1: different dyes were inoculated in the coronal half of root canals or cervical 'gingival' margin, respectively, in separate experiments using the same teeth. Tooth extraction movements were simulated and apical penetration of the dye solutions with and without coronal restorations were examined in each case (20 teeth re-used 4 × ). Part 2: the same procedures were repeated on 30 more teeth but using a standard inoculum of Acidovorax sp. Part 3: 10 teeth with attached periapical lesions were inoculated with Acidovorax sp. in the absence of coronal restorations. Bacterial leakage into the periapical lesions was assessed.

RESULTS

Coronal restorations significantly reduced the flow of dyes (P=0.002) or bacterial suspension (P=0.001) out of the canals and bacterial suspension into (P=0.02) the canals during simulated tooth extraction. The 'size of apical foramina' were positively correlated with passage of bacterial suspension out of the canal (P=0.04) and from the gingival trough into the canal (P=0.008), in the presence of a coronal restoration.

CONCLUSIONS

The presence of coronal restorations, the size of apical foramina and presence of native canal contents with attached periapical lesions, all influenced fluid flow into and out of canals during simulated tooth extraction movements.